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"It's on some secret mission even I'm not supposed to know about."
—Steven Caldwell

(during Enemy at the Gate)

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According to the Stargate Wiki, this is a tie in to SGU:

Joseph Mallozzi confirmed in his blog that the Odyssey's secret mission is Icarus Base related, thus informally introducing Stargate Universe.

Here's the direct answer from said blog entry:

flo writes: “1/Was the odissey’s secret mission from EATG a plan for something ? stargate revolution?”

Answer: Initially, Odyssey’s secret mission was tied to the search for a naquadria-rich planet capable of providing the energy needed to dial Destiny.

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